Organ-specific autoimmune diseases in man are common and cause significant morbidity and mortality. These diseases including type 1 diabetes (IDDM), are chronic and, especially in diabetes, late complications are common. Such diseases are therefore very costly to the individual and, given their estimated prevalence of more than 10% A (lifetime prevalence of IDDM ).3%-1.0%), are very costly to society as well. In contrast to the complexity of human and NOD mouse IDDM, where the large number of genetic factors with relative small effects has complicated the isolation and characterization of these factors, our data suggest that four major genetic factors control IDDM in our crosses in the BB rat model for IDDM (1ddm1-4). The disease process is also influenced by physiological/environmental factors since in the BB rat the animals are lymphopenic from birth but early insulitis is not detected until hyperglycemia and insulin dependency. Our long-term objective is therefore to explain the molecular mechanisms of how these four genetic factors interact to spontaneously induce organ-specific autoimmunity, insulitis and diabetes as well as thyroiditis. We expect that segments of the disease pathway defined by these factors will also be involved in the pathogenesis of other organ-specific autoimmune diseases, and thus help to define organ-specific and organ-independent disease processes. This Program Project application is a competing continuation grant application to continue our collaborative research to positionally clone the lymphopenia (1ddm1/Lyp) gene in the BB rat and uncover the final common pathogenic information pathway that controls IDDM development in the rat. After our initial tremendous progress during the current period (second year out of three years of funding of the present Program Project). We now demonstrate that in the cross between our congenic Dr.Lyp and F344 rats there is one more factor F344 (provisionally named Iddm4), which inhibits the development of diabetes in an otherwise diabetogenic genetic background. Our program project is three highly interactive projects (Seattle, Milwaukee and Cambridge) and our administrative core (Seattle). The projects are: Project 1: Ake Lernmark will (a) complete the identification of the Lyp gene with extensive collaboration with Projects 2 and 3; (b) analyze the lymphopenia, insulitis and thyroiditis phenotypes using the congenic lines Lyp/Lyp/+ and +/+ BB DR, F344/Lyp/Lyp (BCF) and BB/Iddm3/Iddm3 (FCB) rats; (c) develop a mouse in which the Ajm pa gene has been disrupted to determine its function in the thymus (d) map Iddm4. Project 2: Eric S. Lander will collaborator with Projects 1 and 3 by (a) completing the identification of all genes in the mouse and rat Lyp regions by complete genomic sequencing of those regions; (b) rescuing the expression of the Lyp gene in transgenic rats; (c) providing additional sequencing and high-throughput technology support for Iddm3 and further analysis. Project 3: Howard Jacob will use genomic technologies to facilitate the identification of the lymphopenia gene. He will use parallel radiation hybrid and virtual mapping strategies to generate detailed extended comparative maps of Lyp and Iddm3; genomic regions in rat, mouse and human; generated nested deletions of the Lyp region in the mouse and perform functional genomic studies in collaboration with Project 1 on parental (BB DR and F344) and congenic rats (DR/Lyp/Lyp, F344/Lyp/Lyp and Dr. Lyp/Iddm3/Iddm4). The research interactions are well established and shared resources will include parental BB, F344 and our new congenic rats (Project 1), high throughput genome sequencing of the Lyp region rat PAC and mouse BAC contigs (Project 2), rat transgenic rescue (Project 2), homologous recombination of nested deletions in the mouse (Project 3). Our Program Project will identify the lymphopenia gene, determine its role in T cell development and uncover the mechanisms of the final common pathway that is dependent on interactions between Lyp, MHC and Iddm3 to instigate insulitis and diabetes as well as thyroiditis.